메뉴 건너뛰기




Volumn 61, Issue 1, 2012, Pages 1-11

Guided tree topology proposals for Bayesian phylogenetic inference

Author keywords

Bayesian inference; Gibbs sampling; Markov chain Monte Carlo; phylogenetics; posterior probability distribution; tree topology proposals

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; EVALUATION; METHODOLOGY; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; STATISTICAL ANALYSIS;

EID: 84555188629     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr074     Document Type: Article
Times cited : (88)

References (30)
  • 2
    • 0000494208 scopus 로고
    • Hennig's parasitological method: A proposed solution
    • Brooks D.R. 1981. Hennig's parasitological method: a proposed solution. Syst. Zool. 30:229-249.
    • (1981) Syst. Zool. , vol.30 , pp. 229-249
    • Brooks, D.R.1
  • 4
    • 0030539336 scopus 로고    scopus 로고
    • Markov chain monte carlo convergence diagnostics: A comparative review
    • Cowles M.K., Carlin B.P. 1996. Markov chain monte carlo convergence diagnostics: a comparative review. J. Am. Stat. Assoc. 91:883-904.
    • (1996) J. Am. Stat. Assoc. , vol.91 , pp. 883-904
    • Cowles, M.K.1    Carlin, B.P.2
  • 5
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis sampling trees
    • Drummond A., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis sampling trees. BMC Evol. Biol. 7:214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.1    Rambaut, A.2
  • 6
    • 0036021407 scopus 로고    scopus 로고
    • Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    • Drummond A.J., Nicholls G.K., Rodrigo A.G., Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 161:1307-1320. (Pubitemid 34831453)
    • (2002) Genetics , vol.161 , Issue.3 , pp. 1307-1320
    • Drummond, A.J.1    Nicholls, G.K.2    Rodrigo, A.G.3    Solomon, W.4
  • 7
    • 84963088905 scopus 로고
    • A numerical approach to phylogenetic systematics
    • Farris J.S., Kluge A.G., Eckardt M.J. 1970. A numerical approach to phylogenetic systematics. Syst. Zool. 19:172-189.
    • (1970) Syst. Zool. , vol.19 , pp. 172-189
    • Farris, J.S.1    Kluge, A.G.2    Eckardt, M.J.3
  • 10
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings W.K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57:97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 11
    • 22844442543 scopus 로고    scopus 로고
    • Analysis and visualization of tree space
    • DOI 10.1080/10635150590946961
    • Hillis D., Heath T., John K. 2005. Analysis and visualization of tree space. Syst. Biol. 54:471-482. (Pubitemid 41040445)
    • (2005) Systematic Biology , vol.54 , Issue.3 , pp. 471-482
    • Hillis, D.M.1    Heath, T.A.2    St. John, K.3
  • 13
    • 45849120228 scopus 로고    scopus 로고
    • A Bayesian perspective on a non-parsimonious parsimony model
    • DOI 10.1080/10635150802166046, PII 794012413
    • Huelsenbeck J.P., Ane C., Larget B., Ronquist F. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Syst. Biol. 57:406-419. (Pubitemid 351882204)
    • (2008) Systematic Biology , vol.57 , Issue.3 , pp. 406-419
    • Huelsenbeck, J.P.1    Ane, C.2    Larget, B.3    Ronquist, F.4
  • 14
  • 15
    • 1542532208 scopus 로고    scopus 로고
    • Phylogenetic tree construction using markov chain monte carlo
    • Li S., Pearl D.K., Doss H. 2000. Phylogenetic tree construction using Markov chain Monte Carlo. J. Am. Stat. Assoc. 95:493-508.
    • (2000) J. Am. Stat. Assoc. , vol.95 , pp. 493-508
    • Li, S.1    Pearl, D.K.2    Doss, H.3
  • 17
    • 0008766414 scopus 로고    scopus 로고
    • Peskun's theorem and a modifed discrete-state Gibbs sampler
    • Liu J.S. 1996. Peskun's theorem and a modifed discrete-state Gibbs sampler. Biometrika. 83:681-682.
    • (1996) Biometrika , vol.83 , pp. 681-682
    • Liu, J.S.1
  • 18
    • 34547969955 scopus 로고    scopus 로고
    • A geometric approach to tree shape statistics
    • Matsen F.A. 2006. A geometric approach to tree shape statistics. Syst. Biol. 55:652-661.
    • (2006) Syst. Biol. , vol.55 , pp. 652-661
    • Matsen, F.A.1
  • 19
    • 0031498410 scopus 로고    scopus 로고
    • Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo
    • Mau B., Newton M.A. 1997. Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6:122-131.
    • (1997) J. Comput. Graph. Stat. , vol.6 , pp. 122-131
    • Mau, B.1    Newton, M.A.2
  • 21
    • 0042193001 scopus 로고    scopus 로고
    • Ordering and Improving the Performance of Monte Carlo Markov Chains
    • DOI 10.1214/ss/1015346319
    • Mira A. 2001. Ordering and improving the performance of Monte Carlo Markov chains. Stat. Sci. 16:340-350. (Pubitemid 33636355)
    • (2001) Statistical Science , vol.16 , Issue.4 , pp. 340-350
    • Mira, A.1
  • 22
    • 25844516325 scopus 로고    scopus 로고
    • Evolution: Phylogenetic MCMC algorithms are misleading on mixtures of trees
    • DOI 10.1126/science.1115493
    • Mossel E., Vigoda E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science. 309:2207-2209. (Pubitemid 41396068)
    • (2005) Science , vol.309 , Issue.5744 , pp. 2207-2209
    • Mossel, E.1    Vigoda, E.2
  • 23
    • 0015730787 scopus 로고
    • Optimum monte-carlo sampling using markov chains
    • Peskun P.H. 1973. Optimum Monte-Carlo sampling using Markov chains. Biometrika. 60:607-612.
    • (1973) Biometrika , vol.60 , pp. 607-612
    • Peskun, P.H.1
  • 24
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B., Yang Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311. (Pubitemid 26315133)
    • (1996) Journal of Molecular Evolution , vol.43 , Issue.3 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 25
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • DOI 10.1093/bioinformatics/btg180
    • Ronquist F., Huelsenbeck J. 2003. MrBayes 3: Bayesian phy-logenetic inference under mixed models. Bioinformatics. 19: 1572-1574. (Pubitemid 37038874)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 28
    • 84555218755 scopus 로고    scopus 로고
    • The physics of networks
    • February; San Diego
    • Seary A., Richards W. 1997. The Physics of Networks. INSNA Sunbelt XVII; February; San Diego. p. 13-17.
    • (1997) INSNA Sunbelt XVII , pp. 13-17
    • Seary, A.1    Richards, W.2
  • 30
    • 0031669749 scopus 로고    scopus 로고
    • Genealogical inference from microsatel-lite data
    • Wilson I.J., Balding D.J. 1998. Genealogical inference from microsatel-lite data. Genetics. 150:499-510.
    • (1998) Genetics , vol.150 , pp. 499-510
    • Wilson, I.J.1    Balding, D.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.